Hi Daniel,
thanks for checking on your desk. In the meantime I got it working as well. There were different problems together.
One of them which could be interesting for others was that the pin numbering of TWR-SER-SCH.pdf is:

and the readme.txt of flexcan_interrupt demo says something different:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PINS NAME TWR-SER1 CONNECTS TO TWR_SER2
CANL J7 PIN 1 J7 PIN 1
GND J7 PIN 2 J7 PIN 2
CANH J7 PIN 3 J7 PIN 3
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Sure if you have two twr-k64 +twr-ser combos it will work since you are doing the same failure on both sides...
Best Regards,
Johannes